Primary immunodeficiencies (PID) are characterized by alterations in the components of the immune system. The lymphocyte population count by flow cytometry is an approach to molecular diagnosis and is expressed by immunophenotypes. The objective of the study was to describe the lymphocyte population count and immunophenotyping compatible with PID in patients with suspected PID in a Peruvian national reference hospital. Records of 261 cases meeting the Jeffrey Modell Foundation’s PID clinical suspicion criteria were reviewed between April and December of 2016. Of the 261 suspected cases of PID, 54.8% were males. We found 93 patients (35.6%) with PID-compatible immunophenotyping. The common variable immunodeficiency immunophenotype was the most frequent (36.6%), followed by agammaglobulinemias (18.3%). Antibody deficiencies were the most common PID. Other molecular tests are needed for a specific genetic diagnosis.