Capillary malformation (CM; 'port-wine stain'), is a common vascular malformation affecting cutaneous capillary vessels in 0.3% of newborns. Increased incidence of lesions in first-degree relatives of these patients and several reported familial cases suggest that genetic factors may play a role in the pathogenesis of CM. We report the first genome-wide linkage analysis of familial CM. In the non-parametric linkage analysis, strong evidence of linkage (peak Z-score 6.72, P-value 0.000136) was obtained in an interval of 69 cM between markers D5S407 and D5S2098, corresponding to 5q11-5q23. Parametric linkage analysis gave a maximum combined HLOD score of 4.84 (alpha-value 0.67) at marker D5S2044 on 5q15, and analysis using only the linked families, defined a smaller, statistically significant locus CMC1 of 23 cM (peak LOD score 7.22) between markers D5S1962 and D5S652 corresponding to 5q13-5q15. Interesting candidate genes implicated in vascular and neural development, such as MEF2C, RASA1, and THBS4, are in this locus.