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.

According to the state of epiphytic lichens, the preservation of forests and air quality is poor in the entire territory of the Republic of Slovenia, except in forests at higher altitude in the Alps and partially in the Dinaric mountain range.

Acidification of forests represents a potential danger only in the non-hydrocarbon part of Slovenia, especially in the east of the country. According to rough estimates, the critical loads occur particularly in the wider area of both major thermals (Zasavje, Celjska kotlina and Šaleška dolina). Excessive eutrophication of forests for deposition from the air does not take looming forest areas in Slovenia.