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.