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The histomorphometric analysis represents invasive diagnostic method for osteoporosis and other metabolic bone diseases. The manual, semiautomatic and automatic histomorphometric method were compared by analysing the undecalcified bone samples. Validity of the manual method was 0.94, validity of the semiautomatic method was 0.91, validity of the automatic method was 0.67. Reliability of the semiautomatic method according to manual method as reference was 0.85, of the automatic method 0.99. The best result of accuracy was found in manual method, but was not statistically significant. In efficiency there were no statistically significant differences. The manual method proved with results of validity, reliability, accuracy and efficiency seems to be the superior to semiautomatic and automatic histomorphometric method for bone samples.