This study aimed to assess epidemiological trends of Q fever in six countries of Southeast Europe by analysing surveillance data for 2002-2021 period. In this descriptive analysis, we collected and analysed data on confirmed human Q fever cases, obtained from the national Public Health Institutes of Bosnia and Herzegovina, Croatia, Greece, Montenegro, North Macedonia and Serbia. Overall, 2714 Q fever cases were registered during the 20-year period. The crude average annual notification rate was 0.82 (± 2.06) (95% CI: 0.47-1.16) per 100,000 inhabitants, ranged from 0.06 (± 0.04) (95% CI: 0.04-0.08) /100,000 in Greece to 2.78 (± 4.80) (95% CI: 0.53-5.02) /100,000 in the Republic of Srpska (entity of Bosnia and Herzegovina). Significant declining trends of Q fever age standardized rates were registered in Croatia, the Federation of Bosnia and Herzegovina, North Macedonia and Serbia, with an average annual change of -30.15%; -17.13%; -28.33% and - 24.77%, respectively. An unequal spatial distribution was observed. The highest average age-specific notification rate was reported in the 20-59 age group (0.84 (± 0.40) (95% CI: 0.65-1.02) /100,000). Most cases (53.69%) were reported during the spring. Q fever remains a significant public health threat in this part of Europe. The findings of this study revealed the endemic maintenance of this disease in the including countries, with large regional and subnational disparities in notification rates. A downward trend was found in Q fever notification rates across the study countries with the average notification rate higher than in the EU/EEA, during the same period.