The Clinical Classification Software (CCS) consists of two related classification systems, single-level and multi-level, which are designed to meet different needs. Single-level CCS is most useful for ranking of diagnoses and procedures and for direct integration into risk adjustment and other software. Multi-level CCS is most useful when evaluating larger aggregations of conditions and procedures or exploring them in greater detail. CCS documentation provides a listing of the ICD-9-CM codes that are included in each CCS diagnosis and procedure category.

Single-level CCS. This system classifies all diagnoses and procedures into unique groups. The single-level diagnosis CCS aggregates illnesses and conditions into 285 mutually exclusive categories. Most of these categories are homogeneous; for example, CCS category #1 is "Tuberculosis". Some CCS categories combine several less common, individual conditions, such as CCS category #3, which is "Other Bacterial Infections".

Multi-level CCS. The multi-level CCS expands the single-level CCS into a hierarchical system. The multi-level CCS groups single-level CCS categories into broader body systems or condition categories (e.g., "Diseases of the Circulatory System", "Mental Disorders", and "Injury"). It also splits single-level CCS categories to provide more detail. The multi-level system has four levels for diagnoses and three levels for procedures, which provide the opportunity to examine general groupings or to assess very specific conditions and procedures.

For data beginning in the fourth quarter of 2015, the multi-level CCS for ICD-10-CM external cause on morbidity codes is stored in the data element I10_ECauseMCCSn.