Kawasaki disease (KD) is an acute systemic vasculitis of childhood. The diagnosis is based on clinical criteria. However, the presentation of KD is incomplete/atypical for approximately 20 % of patients. Kawasaki disease is complicated with coronary artery lesions (CALs) and considered the most common cause of acquired heart disease in children. The medical records of children discharged with KD from a tertiary pediatric hospital in Athens, Greece, during a decade (2001-2010) were retrospectively analyzed. During the study period, KD was diagnosed for 86 children younger than 14 years of age. Complete diagnostic criteria were fulfilled by 64 of the children (74.4 %), whereas 25.6 % were considered incomplete cases. Cardiovascular complications were detected in 48 children (55.8 %) and CALs in 28 children (32.6 %). The prevalence of CALs did not differ significantly between complete and incomplete/atypical KD (42.2 vs 4.5 %; P = 0.001). Logistic regression analysis showed that erythema in the lips and oral cavity was associated with the development of CALs [odds ratio (OR), 3.03; 95 % confidence interval (CI), 1.051-8.783; P = 0.040]. Conversely, children with incomplete/atypical KD (OR, 0.092; 95 % CI, 0.010-0.816; P = 0.032) and previous antibiotic treatment (OR, 0.17; 95 % CI, 0.036-0.875; P = 0.034) were less likely to experience CALs. Children with an incomplete/atypical presentation of KD or before antibiotic treatment may be at lower risk for the development of CALs. Future multicenter studies may help to establish this association better.