In this paper we develop and study machine learning based models based on latent semantic indexing capable of automatically assigning diagnoses and diagnostic categories to patients based on structured clinical data in their Electronic Health record (EHR). These models can be either used for automatic coding of patient's diagnoses from structured EHR data at the time of discharge, or for supporting dynamic diagnosis and summarization of the patient condition. We study the performance of our diagnostic models on MIMIC-III EHR data.