Delayed diagnosis of stomach, intestines, pancreas, and gallbladder diseases plays a significant role in the complicated non-traumatic peritonitis. The aim of the study was to analyse the causes of fatal peritonitis, and contributing factors to mortality and diagnostic discrepancies. A retrospective study of 52 peritonitis cases from selected 1350 autopsy records in three years was done. We analysed age, sex, length of hospital stays, clinical and pathological diagnosis, complications, comorbidities, laboratory values and diagnostic discrepancies. The results were statistically assessed by Excel and IBM SPSS® Statistics version 26. The most common causes of fatal peritonitis were non-oncological gastrointestinal pathologies (26%), malignancies (23%), pancreas and gallbladder (16%), HIV related (10%), vascular (7%) and other diseases (18%). Mean age of patients at death was 65 years. 61. 4% were males. Median hospitalisation time was two days. Six patients died outside the hospital. In 17.4% cases misdiagnoses were found. Common situations when misdiagnoses had occurred were intestinal ischaemia, malignancies of various origins and perforation of peptic ulcer. Fatal peritonitis was determined by the patient’s delayed hospitalisation with untreated oncological and non-oncological diseases of organs of the abdominal cavity and multiple concomitant diseases. Other contributing factors included not visiting general practitioners and lack of adherence to patients themselves.