A cross-sectional descriptive study was conducted at a dermatology referral centre in Bogotá, to estimate the frequencies and aetiologies of mycoses in the population under 18 years of age attending the medical mycology laboratory over a 13-year period (2000-2012). A total of 1337 samples from 1221 patients were evaluated, involving direct examination and culture for 1279 samples, direct examination alone for 50 and culture alone for 8. During the study period, dermatophytosis was diagnosed via culture in 537 cases (40.1%). The most common aetiological agents were Trichophyton rubrum (235 cases), Microsporum canis (177), Trichophyton mentagrophytes (74) and Microsporum gypseum (22). Pityriasis versicolor was found in 31 cases (5.1%), Candida spp. were found in 17 cases, and non-dermatophyte moulds were confirmed by a second sample in 6 cases (3 cases involving Fusarium spp., 2 Neoscytalidium dimidiatum and 1 Acremonium spp.). In addition, white piedra was diagnosed in 4 cases (0.7%), and tinea nigra in 2 cases (0.3%). Regarding subcutaneous mycoses, 14 cases of sporotrichosis were identified. The results from this study confirm the predominance of dermatophytosis in the paediatric population. T. rubrum and M. canis were the main aetiological agents. We found a few cases of onychomycosis by non-dermatophyte moulds. Sporotrichosis was the only subcutaneous mycosis diagnosed during the study period.