Koštani markeri su veoma korisno dijagnostiško sredstvo, mada je njihova klinička upotreba ograničena specifičnim tehničkim i analitičkim aspektima, kao i njihovom pre-analitičkom varijabilnošću. Koštani markeri, za razliku od mineralne gustine kosti, ukazuju na posebne aspekte kvaliteta kostiju, te stoga nude zasebnu i prognostičku perspektivu u ispitivanju promena mineralne gustine kosti I smanjivanju rizika od fraktura. Smanjenje nivoa koštanih markera usko je povezano sa smanjenjem rizika od frakture vratnih pršljenova usled korišćenja raloksifena, rizedronata i alendronata. Postoje brojne mogućnosti za korišćenje ovih markera u kratkoročnom praćenju toka lečenja osteoporoze, pored merenja mineralne koštane gustine, kako bi se otkrili pacijenti koji ne reaguju na terapiju.
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