The food- and waterborne disease situation in Russia requires special attention. Poor quality of centralized water supplies and sewage systems, biological and chemical contamination of drinking water, as well as contamination of food products, promote widespread infectious diseases, significantly exceeding nationwide rates in the population living in the two-thirds of Russian northern territories. The general aim was to assess the levels of food- and waterborne diseases in selected regions of Russian Arctic, Siberia and the Far East (for the period 2000-2011), and to compare disease levels among regions and with national levels in Russia. This study is the first comparative assessment of the morbidity in these fields of the population of 18 selected regions of Russian Arctic, Siberia and the Far East, using official statistical sources. The incidences of infectious and parasitic food- and waterborne diseases among the general population (including indigenous peoples) have been analyzed in selected regions (per 100,000 of population, averaged for 2000-2011). Among compulsory registered infectious and parasitic diseases, there were high rates and widespread incidences in selected regions of shigellosis, yersiniosis, hepatitis A, tularaemia, giardiasis, enterobiasis, ascariasis, diphyllobothriasis, opistorchiasis, echinococcosis and trichinellosis. Incidences of infectious and parasitic food- and waterborne diseases in the general population of selected regions of the Russian Arctic, Siberia and the Far East (2000-2011) are alarmingly high. Parallel solutions must be on the agenda, including improvement of sanitary conditions of cities and settlements in the regions, modernization of the water supply and of the sewage system. Provision and monitoring of the quality of the drinking water, a reform of the general healthcare system and the epidemiological surveillance (including gender-divided statistics), enhancement of laboratory diagnostics and the introduction of preventive actions are urgently needed.