diff --git a/js/llm.ts b/js/llm.ts
index 4682a4e..0c65c77 100644
--- a/js/llm.ts
+++ b/js/llm.ts
@@ -51,6 +51,16 @@ export function templateUsesThreadVariables(template: string): boolean {
   return THREAD_VARIABLE_PATTERN.test(template);
 }
 
+function filterSystemMessagesFromThread(thread: unknown[]): unknown[] {
+  return thread.filter((message) => {
+    if (!message || typeof message !== "object" || Array.isArray(message)) {
+      return true;
+    }
+    const role = Reflect.get(message, "role");
+    return role !== "system";
+  });
+}
+
 const NO_COT_SUFFIX =
   "Answer the question by calling `select_choice` with a single choice from {{__choices}}.";
 
@@ -311,7 +321,8 @@ export function LLMClassifierFromTemplate<RenderArgs>({
     let threadVars: Record<string, unknown> = {};
     if (runtimeArgs.trace && templateUsesThreadVariables(promptTemplate)) {
       const thread = await runtimeArgs.trace.getThread();
-      const computed = computeThreadTemplateVars(thread);
+      const scorerThread = filterSystemMessagesFromThread(thread);
+      const computed = computeThreadTemplateVars(scorerThread);
       // Build threadVars from THREAD_VARIABLE_NAMES to keep in sync with the pattern
       for (const name of THREAD_VARIABLE_NAMES) {
         threadVars[name] = computed[name as keyof ThreadTemplateVars];
diff --git a/py/autoevals/llm.py b/py/autoevals/llm.py
index e3a6482..c69d273 100644
--- a/py/autoevals/llm.py
+++ b/py/autoevals/llm.py
@@ -64,6 +64,7 @@
 from .thread_utils import (
     THREAD_VARIABLE_NAMES,
     compute_thread_template_vars,
+    filter_system_messages_from_thread,
     template_uses_thread_variables,
 )
 
@@ -427,7 +428,7 @@ def _compute_thread_vars_sync(self, trace) -> dict[str, object]:
         if not isinstance(thread, list):
             thread = list(thread)
 
-        computed = compute_thread_template_vars(thread)
+        computed = compute_thread_template_vars(filter_system_messages_from_thread(thread))
         return {name: computed[name] for name in self._thread_variable_names}
 
     async def _compute_thread_vars_async(self, trace) -> dict[str, object]:
@@ -443,7 +444,7 @@ async def _compute_thread_vars_async(self, trace) -> dict[str, object]:
         if not isinstance(thread, list):
             thread = list(thread)
 
-        computed = compute_thread_template_vars(thread)
+        computed = compute_thread_template_vars(filter_system_messages_from_thread(thread))
         return {name: computed[name] for name in self._thread_variable_names}
 
     def _request_args(self, output, expected, **kwargs):
diff --git a/py/autoevals/thread_utils.py b/py/autoevals/thread_utils.py
index e816348..bdfb13c 100644
--- a/py/autoevals/thread_utils.py
+++ b/py/autoevals/thread_utils.py
@@ -38,6 +38,10 @@ def is_llm_message_array(value: Any) -> bool:
     return isinstance(value, list) and all(is_role_content_message(item) for item in value)
 
 
+def filter_system_messages_from_thread(thread: list[Any]) -> list[Any]:
+    return [message for message in thread if not (isinstance(message, Mapping) and message.get("role") == "system")]
+
+
 def _indent(text: str, prefix: str = "  ") -> str:
     return "\n".join(prefix + line for line in text.split("\n"))