SI-3: Malicious Code Protection

To meet the si-3: malicious code protection requirement, you must deploy and operate malware prevention and detection controls at system entry and exit points (endpoints, email, web, network egress/ingress, file transfer paths) and prove they detect and eradicate malicious code. Operationalize SI-3 by defining coverage, enforcing policy-based configuration, monitoring alerts, and retaining evidence that the controls run as designed.

Key takeaways:

• SI-3 is about control placement (entry/exit points) and outcomes (detect + eradicate), not just buying an antivirus tool.
• Auditors expect end-to-end coverage mapping plus proof of continuous operation (updates, alerts, response actions).
• The fastest path to readiness is a repeatable evidence set tied to a named owner, procedure, and recurring extracts ¹.

SI-3 is one of those requirements that looks simple on paper (“have anti-malware”), but fails in audits because teams cannot show consistent coverage across the real paths malware enters and leaves your environment. The control asks for protection mechanisms at system entry and exit points and expects you to operate them so they can detect and eradicate malicious code ². That means the compliance burden is less about the brand of tool and more about execution: where you placed it, what it blocks or quarantines, how you keep it current, what happens when it fires, and how you prove all of that.

For a CCO or GRC lead, the goal is to make SI-3 auditable without turning it into an endless technical program. You need a scoped inventory, a short set of standard configurations, an exception process for assets that cannot run agents, and an evidence cadence that survives staff turnover. If you run third-party hosted systems, managed endpoints, or cloud services, SI-3 also becomes a shared-responsibility exercise: you must validate what the third party covers and what you still own.

Regulatory text

Requirement (verbatim excerpt): “Implement {{ insert: param, si-03_odp.01 }} malicious code protection mechanisms at system entry and exit points to detect and eradicate malicious code;” ²

Operator interpretation:
You must implement malware controls in the places malware enters your system (ingress) and where data/software leaves (egress). “Detect” implies prevention and/or identification (signatures, heuristics, reputation, sandboxing, behavioral detection). “Eradicate” implies an action that removes the malware from the environment (quarantine, delete, isolate host, remediate persistence, reimage, or block further execution) and a process to execute those actions reliably.

Plain-English interpretation (what SI-3 is really asking)

SI-3 expects you to answer four audit questions with evidence:

1. Where can malware enter or exit? Email, web browsing, removable media, file uploads/downloads, API payloads, remote access, SaaS connectors, CI/CD artifacts, and vendor-managed connections.
2. What controls are in those paths? Endpoint protection, email security, web proxy/secure web gateway, network malware inspection, EDR, file scanning, container/image scanning where relevant, and egress filtering.
3. Do they run correctly over time? Updates, policy enforcement, logging, alert routing, tuning, and coverage for new assets.
4. Do you act on detections? Quarantine/isolation workflows, incident tickets, root-cause follow-up, and restoration steps.

Who it applies to (entity + operational context)

SI-3 applies to:

• Federal information systems and programs aligned to NIST SP 800-53 ¹.
• Contractor systems handling federal data, including environments supporting federal contracts where 800-53 controls are imposed through contract, SSPs, or agency baselines ¹.

Operationally, it applies wherever your “system” boundary includes:

• Corporate endpoints (managed laptops/desktops), servers, and VMs.
• Cloud workloads (IaaS/PaaS), containers, and build pipelines that produce deployable artifacts.
• Email and collaboration platforms.
• Network edges: VPN, ZTNA gateways, ingress controllers, web gateways, and egress points.
• High-risk conduits with third parties (managed service providers, file exchange, EDI, shared drives, remote administration).

What you actually need to do (step-by-step)

1) Name the control owner and define the “system entry/exit points”

Create a one-page SI-3 control record:

• Owner: usually Security Operations (SOC) or Endpoint/Platform Security, with GRC as accountability for evidence.
• In-scope systems: align to your authorization boundary / SSP scope.
• Entry points: inbound email, web traffic, remote access, file uploads, removable media, inbound integrations.
• Exit points: outbound web, email sending, file exports, API egress, admin channels, data exfil paths.

Deliverable: “Entry/Exit Point Coverage Map” (table) that links each point to the protection mechanism and logging source.

2) Standardize the protection stack by asset class

Define minimum required controls per class, for example:

• Endpoints: EPP/EDR with real-time scanning, behavior monitoring, quarantine, tamper protection.
• Servers: EDR (agent or sensor), scheduled scans where appropriate, application allowlisting where feasible.
• Email: attachment scanning, link rewriting/time-of-click checks, anti-phishing controls.
• Web: secure web gateway/proxy with malware scanning and reputation blocking.
• Cloud/storage: malware scanning for object uploads/downloads where applicable; scanning of shared file repositories.
• CI/CD artifacts: scan dependencies and produced artifacts before release when those artifacts can carry malware.

Keep it policy-level: specify required capabilities and evidence, not vendor marketing features.

3) Configure for “detect and eradicate,” not “alert-only”

Set required actions for high-confidence detections:

• Automatic quarantine/isolation for endpoint detections when safe.
• Block at gateway for known malicious downloads/URLs.
• Attachment detonation or blocking for risky file types.
• Containment playbook for high-severity events (isolate host, reset credentials, collect forensics, reimage if needed).

Define what “eradicate” means in your environment:

• Quarantine/delete plus verification scan, or
• Reimage and restore from known-good baselines, or
• Remove persistence mechanisms and validate via EDR telemetry.

4) Build coverage assurance (the part auditors focus on)

Implement controls that ensure new assets cannot slip through:

• Endpoint management enrollment gates (devices must enroll to get access).
• Cloud workload onboarding requirements (agent installed or compensating control documented).
• Exceptions process for assets that cannot run agents (OT, legacy, appliances). Require a compensating control at the boundary (network inspection, restricted connectivity, jump host, allowlisting).

Maintain a living coverage report: asset inventory vs. agent installed vs. last check-in vs. policy compliance.

5) Wire alerts into incident handling and prove follow-through

SI-3 will be tested through your ticketing and response trail.

• Route malware detections to a monitored queue (SOC, IT Ops with escalation).
• Require tickets for significant detections with: affected asset, user, time, action taken, containment, eradication steps, and closure notes.
• Track recurring issues (same host, same user behavior, same third-party conduit).

6) Establish the evidence cadence

Decide what you will produce on a recurring basis so audits don’t become archaeology:

• Monthly (or other consistent interval you choose): coverage reports, update compliance, high-severity detection summary.
• Per event: incident/ticket trail showing eradication actions.
• Per change: policy/configuration change approvals and testing notes.

Daydream (as a workflow, not a tool swap) helps by mapping SI-3 to a named owner, a written procedure, and recurring evidence artifacts so you can answer the same audit questions the same way every cycle ¹.

Required evidence and artifacts to retain

Keep evidence that proves placement, operation, and response.

Design / governance artifacts

• SI-3 control statement (scope, owner, tools, entry/exit points)
• Malware protection standard (required capabilities by asset class)
• Exception register with compensating controls and approvals
• Network/data flow diagram or entry/exit coverage map

Operational artifacts (high audit value)

• Endpoint/EDR coverage export (inventory, agent status, last check-in)
• Policy configuration snapshots (real-time protection on, quarantine enabled, tamper protection)
• Update status reports (signature/engine versions where applicable)
• Email/web gateway reports showing blocked malware and policy enforcement
• Sample alert-to-ticket chain demonstrating detect → triage → eradicate → close
• Incident response playbooks/runbooks for malware events

Common exam/audit questions and hangups

• “Show me your system entry and exit points and the control at each point.”
  Hangup: teams list tools but cannot map them to specific conduits.
• “How do you know every endpoint/server is protected?”
  Hangup: no coverage report; reliance on “should be installed.”
• “What happens when malware is detected?”
  Hangup: alerts exist, but no consistent eradication steps or ticket evidence.
• “How do you handle systems that cannot run agents?”
  Hangup: exceptions exist informally; no compensating controls.

Frequent implementation mistakes (and how to avoid them)

1. Treating SI-3 as endpoint antivirus only.
   Fix: document and implement controls at email/web ingress and network/cloud egress points where malware traverses.
2. No definition of “eradicate.”
   Fix: write a short eradication standard (quarantine vs. reimage vs. cleanup) and tie it to ticket closure requirements.
3. Evidence is screenshots.
   Fix: prefer exports (CSV/PDF reports) on a recurring cadence plus immutable ticket history.
4. Exceptions become a back door.
   Fix: time-bound exceptions, require compensating controls, and review them on a regular schedule you can defend.
5. Third-party coverage assumptions.
   Fix: require third parties to attest to malware controls for the portions they operate, and document your residual responsibility for endpoints, identity, and data paths.

Enforcement context and risk implications

No public enforcement cases were provided in the source catalog for SI-3, so this page does not cite specific actions. Practically, SI-3 gaps raise breach and operational resilience risk: malware often becomes the entry point for credential theft, ransomware, and data exfiltration. In assessments, weak SI-3 evidence usually shows up as “control not implemented” or “not operating effectively” because teams cannot demonstrate coverage or consistent remediation.

Practical 30/60/90-day execution plan

First 30 days (stabilize and prove basic coverage)

• Assign SI-3 owner and publish a one-page control statement aligned to entry/exit points ².
• Build the entry/exit coverage map and identify gaps (email, web, endpoints, servers, cloud uploads).
• Produce your first repeatable evidence set: endpoint coverage export, policy configuration snapshot, and a sample malware ticket showing eradication steps.
• Stand up an exceptions register with compensating controls and approvals.

Days 31–60 (close gaps and harden operations)

• Expand coverage to unprotected asset classes (servers, VDI, cloud workloads) and formalize onboarding gates.
• Standardize alert routing and ticket templates so eradication actions are consistently recorded.
• Tune policies for safe automatic actions (quarantine/isolation) and document when manual action is required.
• Validate third-party responsibilities for malware protection where they operate parts of your system boundary.

Days 61–90 (make it audit-proof and sustainable)

• Run a tabletop or operational drill using a real detection scenario to validate detect → eradicate → evidence.
• Establish recurring reporting and review: coverage, exceptions, and high-severity malware events.
• Document key metrics qualitatively (trend direction, recurring root causes) without inventing numeric targets.
• Implement the “map to owner + procedure + recurring artifacts” pattern in Daydream so SI-3 stays current through tool changes and org changes ¹.

Frequently Asked Questions

Does SI-3 require antivirus on every single system?

SI-3 requires malicious code protection at system entry and exit points to detect and eradicate malicious code ². For systems where agents are not feasible, document a compensating control at the boundary and retain the approved exception.

What counts as a “system entry and exit point” in a cloud-first environment?

Treat email, web ingress/egress, file upload/download paths (object storage, collaboration tools), remote access gateways, and CI/CD artifact flows as entry/exit points. Map each conduit to a specific control and a log source you can export for evidence.

What evidence satisfies “eradicate malicious code”?

Keep incident records that show the detection and the remediation action taken (quarantine/delete, host isolation, reimage, or other defined process). Auditors typically accept a clear alert-to-ticket chain plus proof the endpoint/workload returned to a known-good state.

We outsource IT to a third party. Who owns SI-3?

You still own the requirement outcome for your system boundary, even if the third party operates the tools. Require the third party to provide coverage reports, configuration attestations, and incident records that demonstrate detect-and-eradicate actions.

How do we handle developer laptops and ephemeral build runners?

For developer laptops, enforce managed endpoint controls and block access for non-enrolled devices. For ephemeral runners, use hardened images and scanning of artifacts before release, and retain pipeline logs and scan outputs as the evidence trail.

How should a GRC team operationalize SI-3 without becoming the SOC?

GRC should own the control narrative, scope, and evidence cadence, while Security/IT owns configuration and response. Daydream helps by mapping SI-3 to a named owner, implementation procedure, and recurring evidence artifacts so audits become a packaging exercise, not an investigation ¹.

Footnotes

1. NIST SP 800-53 Rev. 5

2. NIST SP 800-53 Rev. 5 OSCAL JSON