We describe an automated multidimensional approach for the analysis of flow cytometry data based on pattern classification. Flow cytometry is a widely used technique both for research and clinical purposes where it has become essential for the diagnosis and follow up of a wide spectrum of diseases, such as HIV-infection and neoplastic disorders. Flow cytometry data sets are composed of quite a large number of observations that can be viewed as elements of a n-dimensional space. The aim of the analysis of such data files is typically to classify groups of cellular events as specific populations with biological meaning. Despite significant improvements in data acquisition capabilities of flow cytometers, data analysis is still based on bi-dimensional strategies which were defined a long time ago. These are strongly dependent on the expertise of an expert operator, this approach being relatively subjective and potentially leading to unreliable results. Automated analysis of flow cytometry data is an essential step to improve reproducibility of the results. The proposed automated analysis was implemented on peripherial blood lymphocyte subsets from 307 samples stained and prepared in an identical way and it was capable of identifying all cell subsets present in each sample studied that could also be detected in the same data files by an expert operator. A highly significant correlation was found between the results obtained by an expert operator using a conventional manual method of analysis and those obtained using the implemented automated approach.