Peritonsillar abscess (PTA) is a frequent complication to acute tonsillitis, in particular in adolescents and young adults. Smoking is most commonly initiated during adolescence and young adulthood. The study examines whether smoking increases the risk of PTA and whether smoking is associated with the bacterial findings in PTA. All patients with PTA admitted to the Ear-Nose-Throat Department at Aarhus University Hospital from January 2001 through December 2006 were included in the study. Age- and gender-stratified data on smoking habits in the Danish population and demographic data for Aarhus County for the same 6 years were obtained. Smoking status was available for 679 (80 %) of 847 patients with PTA. 247 (36 %) patients admitted to daily tobacco smoking. Age-stratified odds ratios of smokers compared to non-smokers, for developing PTA, were in the range of 1.9-4.7. Fusobacterium necrophorum and beta-hemolytic streptococci were equally distributed between smokers and non-smokers. Twenty nine percent of the higher incidence of PTA among males compared to females could be explained by a higher prevalence of smoking in males. After correcting for differences in smoking prevalence by gender, the risk of PTA was calculated to be 9.5 % higher among males than females. Smoking was associated with significantly increased risk of PTA in both males and females of all ages. No differences in the microbiological flora of smokers and non-smokers with PTA were found.