Despite the important nail alterations caused by onychomycosis and psoriasis few studies have characterized the microstructure of the diseased nail plate and the diffusion and penetration of drugs through this altered structure. This work aimed to characterize the microstructure of the healthy, onychomycotic and psoriatic human nail using Raman spectroscopy, scanning electron microscopy, optical microscope profilometry and mercury intrusion porosimetry followed by analysis of the structure with PoreCor® software. The results showed that onychomycotic nails have higher porosity and lower amounts of disulphide bonds compared to healthy nails. This suggests that the presence and action of fungi on the nail plate makes this structure more permeable to water and drugs. Psoriatic nails had increased porosity compared to healthy nails but lower than fungal infected specimens. In vitro permeation studies showed that diseased nails were more permeable to ciclopirox (onychomycosis) and clobetasol (psoriasis) although drug permeation was highly variable and likely to be influenced by the degree of alteration of the nail structure. On the whole, this work provides new and valuable information about the microstructure and porosity of diseased nails and a plausible explanation of the increased drug permeability observed in this work and elsewhere.