Invasive fungal infections are becoming an increasing public health problem owing to the growth in numbers of susceptible individuals. Despite this, the profile of mycoses remains low and there is no surveillance system specific to fungal infections currently existing in England and Wales. We analysed laboratory reports of deep-seated mycoses made to the Communicable Disease Surveillance Centre between 1990 and 1999 from England and Wales. A substantial rise in candidosis was seen during this period (6·76–13·70 reports per million population/year), particularly in the older age groups. Rates of cryptococcosis in males fluctuated over the decade but fell overall (1·05–0·66 per million population/year), whereas rates of female cases gradually rose up until 1998 (0·04–0·41 per million population/year). Reports of Pneumocystis carinii in men reduced substantially between 1990 and 1999 (2·77–0·42 per million population/year) but showed little change in women. Reports of aspergillosis fluctuated up until 1996, after which reports of male and female cases rose substantially (from 0·08 for both in 1996 to 1·92 and 1·69 per million population/year in 1999 for males and females respectively), largely accounted for by changes in reporting practice from one laboratory. Rates of invasive mycoses were generally higher in males than females, with overall male-to-female rate ratios of 1·32 (95% CI 1·25–1·40) for candidosis, 1·30 (95% CI 1·05–1·60) for aspergillosis, 3·99 (95% CI 2·93–5·53) for cryptococcosis and 4·36 (95% CI 3·47–5·53) for Pneumocystis carinii. The higher male than female rates of reports is likely to be a partial reflection of HIV epidemiology in England and Wales, although this does not fully explain the ratio in infants and older age groups. Lack of information on underlying predisposition prevents further identification of risk groups affected. Whilst substantial under-reporting of Pneumocystis carinii and Cryptococcus species was apparent, considerable numbers of superficial mycoses were mis-reported indicating a need for clarification of reporting guidelines. Efforts to enhance comprehensive laboratory reporting should be undertaken to maximize the utility of this approach for surveillance of deep-seated fungal infections.