The aim of the study is to present the second most frequent cause of death in Athens, during the German Occupation (1941-1944), which was the infectious diseases. Until now the majority of studies have focused to the great famine of 1941-42 with thousands of victims. Although the famine was the main cause of death, a significant number of cases were due to infection diseases or noncommunicable diseases. The study was based on the archives, such as the books of admissions of the hospitals located in Athens, but also to the official public records of the Prefecture of Athens. From the study of the archival material it is evident that tuberculosis, malaria, epidemic typhus, typhoid fever and meningitis, were the most important causes of morbidity and mortality. During the German Occupation, tuberculosis and malaria significantly increased. While epidemic outbreaks reported of epidemic typhus (1941), malaria (1942) and food-born poisoning of bacterial etiology (1941, 1942 and 1943). It is worth mentioning that there was an increase of syphilis, genital warts, pediculosis and scabies. The topographic study indicated that the southwest and southeast areas of the Municipality of Athens, and the bordering Municipalities, were areas with higher morbidity and mortality. These areas were the residence of the working social class and the refugees from the Asia Minor (1922). The increase of morbidity and mortality in these areas can be explained by the low social-economic living conditions, since the Interwar period, the deterioration due to the Occupation, and the population density. The spectrum of the infectious diseases in Athens was not significantly different from that of Interwar. The difference was the increase of the cases due to the miserable living conditions and the collapse of the public services for the surveillance and control of the infectious diseases.