To optimize the mapping of alteration zones as a component of exploration for many types of mineral deposits, mineralogical determination of alteration types is compared with an estimation of alteration types based on chemical data using the prize-penalty function, G = nψ (1 − γΣΣη ij φ ij), where G is gain of the system, and n, ψ, γ, ( η ij), and ( φ ij) are number of samples, value of prize, penalty coefficient, matrix showing identification probability, and matrix showing penalty, respectively. The subscripts i and j indicate that a sample belonging to group i appears to belong to group j. The diagonal elements of both matrices correspond to correct identification, while the other elements to misidentification. A large value of an element of an penalty matrix means undesirable misidentification. A penalty coefficient and each element of a penalty matrix are given in accordance with the purpose of an exploration program. The data used in this work were provided by the Metal Mining Agency of Japan which chemically analyzed 533 rock samples from the Kushikino area, southwestern Japan, and identified the constituent minerals of 349 of the samples by X-ray powder diffraction. The samples were divided into two groups and six types: a first group of LA (least altered), SZ (smectite-zeolite) and PR (propylitic) types formed by regional hydrothermal activity; a second group of MC (mica-chlorite), AG (argillic), and KM (kaolinite-mica) types associated with gold mineralization. Results suggest that for this case, under the assumption used, classification of samples is more effective by an estimation procedure based on chemical data than by mineralogical determination, provided that some misidentification of altered samples is acceptable.