Instructions for Coding Primary Site

Coding instructions for Primary Site are found in several resources. Each of these will be described briefly. Refer to the resource itself for more information.

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ICD-O Primary Site Coding Rules

ICD-O provides several rules for the coding and guidelines for topography and morphology. These rules are defined in the Introduction section of ICD-O. Topography guidelines are labeled A-E.

  • Topographic regions and ill-defined sites
  • Prefixes
  • Malignant neoplasm overlapping site boundaries
  • Topography codes for lymphomas
  • Topography code for leukemias

SEER Program Coding and Staging Manual Primary Site Coding Rules

SEER provides guidelines for coding primary site in an abstract in the SEER Program Coding and Staging Manual.

  • Unless otherwise instructed, use all available information in the medical record to code the site.
  • Code the site in which the primary tumor originated, even if it extends onto/into an adjacent subsite.
  • Code the last digit of the primary site code to ‘8’ when a single tumor overlaps an adjacent subsite(s) of an organ and the point of origin cannot be determined.
  • Code the site of the invasive tumor when there is an invasive tumor and in situ tumor in different subsites of the same anatomic site.
  • Code the last digit of the primary site code to ‘9’ for single primaries when multiple tumors arise in different subsites of the same anatomic site and the point of origin cannot be determined.
  • Some histology/behavior terms in ICD-O-3 have a related site code in parentheses. Code the site as documented in the medical record and ignore the suggested ICD-O-3 code when a primary site is specified in the medical record.
  • Code the primary site, not the metastatic site. If a tumor is metastatic and the primary site is unknown, code the primary site as unknown (C809).
  • When the medical record does not contain enough information to assign a primary, consult a physician advisor to assign the site code. If a physician advisor cannot identify a primary site, use the NOS category for the organ system or the Ill-Defined Sites (C760-C768).
  • When there are two or more possible primary sites documented and all are within the same system, assign the NOS code for the body system
  • Specific guidelines for coding Sarcoma and Gastrointestinal Stromal Tumors (GIST) are provided in the SEER Program Coding and Staging Manual.
  • Code Unknown Primary Site (C809) if there is not enough information to assign an NOS or Ill-Defined Site category. C809 is a code of last resort. Only use C809 when all other guidelines cannot be applied.

Additional site-specific coding guidelines are available on the SEER website.

SEER Coding Guidelines Primary Site Coding Rules

SEER provides site-specific Coding Guidelines in Appendix C of the SEER Program Coding and Staging Manual. Some of the coding guidelines include site-specific information about coding primary site. Refer to these guidelines for additional primary site coding instructions.

Sites with primary site coding guidelines in Appendix C:

  • Esophagus
  • Colon
  • Lung
  • Breast
  • Bladder
  • Kaposi sarcoma

The SEER Coding and Staging Manual, Appendix C can be found on the SEER Website:

Hematopoietic and Lymphoid Neoplasm Coding Manual (Heme manual) and the Hematopoietic and Lymphoid Neoplasm Database (Heme DB) Primary Site Coding Rules

Instructions for assigning primary site for hematopoietic and lymphoid neoplasms are included in the Heme manual. These instructions correspond to the primary site and histology (PH) rules in the Heme manual and to information in the Heme DB.

Solid Tumor Rules Primary Site Coding Rules

The purpose of these rules is to determine the number of primaries and to code histology.  The Solid Tumor Rules are not the principal reference for primary site coding instructions; however, there are some primary site coding instructions in the following site-specific rules.

  • Head and Neck
  • Cutaneous Melanoma
  • Lung
  • Breast
  • Urinary
  • Malignant CNS
  • Non-malignant CNS

Updated: December 13, 2023