In this paper different aspects of value-at-risk estimation are considered. Daily returns of CISCO, INTEL and NASDAQ stock indices are analyzed for period: September 1996 - September 2006. Methods that incorporate time varying variability and heavy tails of the empirical distributions of returns are implemented. The main finding of the paper is that standard econometric methods underestimate the value-at-risk parameter if heavy tails of the empirical distribution are not explicitly taken into account. .