The infection of Lithuanian honey bee colonies by Nosema apis and N. ceranae and the consequences were analysed over a four-year (2011 - 2014) period. Both mono-infection either by N. apis or N. ceranae, and co-infection by both Nosema species, were found. There was a decrease in the percentage of Nosema infected colonies during the four-year study period. There were fewer colonies infected by N. ceranae, whereas the number of colonies with N. apis remained approximately at the same level during the study. The prevalence of both types of Nosema in honey bee colonies varied seasonally, i.e. there was a higher percentage of colonies infected in spring and summer but very rarely was Nosema detected in autumn. Mono-infection by N. apis, and co-infection by both Nosema species, were significantly more often recorded in weak and moderate colonies than in strong colonies. Mono-infection by N. ceranae was more often detected in weak colonies than in moderate and strong colonies, but more often detected in strong than in moderate colonies. A moderate link between a high prevalence of N. ceranae infection and an increased risk for winter colony mortality was observed.