Incomplete Kawasaki disease (KD) is associated with delayed diagnosis and treatment, which in turn can lead to the development of coronary artery lesions (CALs). The aim of this study was to determine the epidemiological features of incomplete KD compared with complete KD and to identify risk factors for CALs from incomplete KD patients using data from a nationwide survey of 2007-2008 in Japan. A total of 23,263 patients were classified according to the number of principal clinical signs: 80% (n = 18,620) had complete forms of KD, 14.2% had four principal signs, 4.6% had three signs, and 1.2% had only one or two signs. In comparison with complete KD cases, the prevalence of CAL development tended to be larger and the proportion receiving initial intravenous immunoglobulin (IVIG) treatment were significantly smaller in patients with incomplete forms. In addition, hospital attendance after 7 days of illness or later was significantly associated with CAL development in all incomplete groups (OR: 2.52 in total patients with incomplete KD, 3.26 in those with one or two principal signs, 2.94 in those with three signs, 2.35 in those with four signs). The higher prevalence of CALs in incomplete KD reflects difficulties in diagnosis and delays in treatment. More timely diagnosis and treatment of incomplete KD patients could further prevent the development of cardiac lesions.