Asthma has become the most common chronic disease among children and is one of the major causes of hospitalisation of children under the age of 15. In the period 1999–2004, asthma prevalence among children in the EU varied from less than 5% to over 20%. Most hospital admissions of children with asthma occur in Ljubljana and Maribor. As more and more people are sensitive to allergens, allergic diseases may increase in Europe in the coming years.

Slovenia reported 1–3 waterborne outbreaks per year during 2008–2017; there were no reports in 2009, 2015, and 2017. In these outbreaks, associated with drinking water, 5–355 cases were reported. Some outbreaks had unidentified etiologies, some were caused by Cryptosporidium parvum, Escherichia coli, rotaviruses, noroviruses, Bacillus cereus, Campylobacter jejuni, Salmonella Typhimurium.

Due to external air pollution by ozone, leaf injuries of the ozone-sensitive clone of white clover were visible in Ljubljana, Rakičan pri Murski Soboti and Iskrba pri Kočevski Reki in the period 2000-2007.

In recent years, cadmium and lead concentrations in the kidneys and livers of roe deer has decreased below the level of toxic concentrations that could have a direct adverse effect on the health of the individuals of this species. Nevertheless, cadmium concentrations in the internal organs of roe deer exceed the admissible concentration determined by law in many areas of Slovenia (taking into consideration the suitability for human consumption).