Foodborne infections remain a significant public health concern in Slovenia and globally. In 2023, the incidence of these infections in Slovenia decreased by 7% compared to 2022, with viral intestinal infections being the most common. Among bacterial pathogens, Campylobacter, Clostridioides difficile, Salmonella, and pathogenic E. coli are predominant. The World Health Organization estimates that at least one in ten people worldwide contracts a foodborne infection each year, representing a substantial burden on public health.

In 2022, drinking water monitoring was carried out for 93.8% of Slovenia's population across 863 supply zones that serve 50 or more people. Large and medium-sized zones, serving more than 500 inhabitants, generally maintain a good water quality. The greatest issues are found in smaller zones (50-500 inhabitants) with a higher percentage of fecally contaminated samples. Chemical contamination was detected in two zones, mainly due to exceeded levels of lead and the pesticide desethyl-atrazine.

Lyme borreliosis (LB) and tick-borne encephalitis (TBE) are the most common vector-borne diseases transmitted by ticks. Between 2014 and 2023, Slovenia reported annually slightly less than 3,000 to over 7,000 cases of LB and an average of 105 TBE cases (the highest in 2020 - 187 cases, the lowest in 2015 and 2021 - 62 cases). Due to climate change, which influences the expansion of tick habitats and extends their activity season, the risk of infection may increase in the future. Increased awareness and individual prevention are key factors in reducing the burden of both diseases.

In Slovenia, between 2012 and 2022, 1 to 3 waterborne outbreaks were reported annually, except in the years 2015 and 2017–2020, when no outbreaks were reported. In individual outbreaks, between 3 and 355 cases were reported. In about half of these outbreaks, the causative agent was not identified. Confirmed causative agents included Cryptosporidium parvum, Escherichia coli, rotavirus, norovirus, Bacillus cereus, Campylobacter jejuni, Salmonella Typhimurium, and Francisella tularensis.

The average concentrations of dioxins and dl-PCBs in fish and seafood are the highest among all foods, followed by other animal-derived foods. Long-term average exposure of the Slovenian population to dioxins due to fish consumption does not exceed the Tolerable Weekly Intake (TWI), except for infants and toddlers, indicating a higher health risk for the most vulnerable groups. When considering only fish consumers, exposure to dioxins and PCBs exceeds the TWI in all age groups.