The aim of this study was to describe the clinical profile of children with congenital pigmentary anomalies along Blaschko lines and the associated manifestations in the central nervous system. Twenty-six children aged 12 years or less (14 boys and 12 girls), with hypopigmentation and hyperpigmentation along Blaschko lines and central nervous system manifestations were included during the period June 2001 to December 2003. Detailed physical, cutaneous, and systemic examinations were carried out. Relevant investigations included histopathology, karyotyping, electroencephalogram, computerized tomography scans, and magnetic resonance imaging of the brain whenever possible. Twenty children had hyperpigmentation along the lines of Blaschko, four had hypopigmentation, and two had a combination of the two. Eight children had diffuse involvement. Of these, two each had hypomelanosis of Ito, incontinentia pigmenti and linear and whorled nevoid hypermelanosis. The remaining 20 patients could not be categorized as any of the described entities. The majority (92.3%) of patients manifested skin and central nervous system disorders before the age of 2 years. Hyperpigmentation along Blaschko lines was significantly higher in patients with central nervous system manifestations (p = 0.01). Developmental delay was the most frequent central nervous system presentation. Multiple systems were affected, including the eyes. Histology was useful to distinguish incontinentia pigmenti from other types of nevoid hyperpigmentation.