We have carried out multi-epoch VLBI observations of the H2O maser sources associated with young stellar objects (YSOs) in nearby molecular clouds with VERA (VLBI Exploration of Radio Astrometry), which is a newly constructed VLBI network in Japan (Kobayashi et al. 2003). The main goal of our study is to measure the absolute proper motions and distances to nearby molecular clouds within 1 kpc from the Sun, to reveal their 3-dimensional structures and dynamical properties. Using the VERA dual-beam receiving system (Honma et al. 2003), we have carried out phase-referencing VLBI observations and measured annual parallaxes and absolute proper motions of the H2O maser features with respect to the extragalactic radio sources. We have successfully detected the annual parallax of one of the H2O maser features in Orion KL to be 2.29±0.10 mas, corresponding to the distance of 437±19 pc from the Sun (Hirota et al. 2007). In addition, the annual parallax of SVS13 in NGC 1333 is also determined to be4.10±0.17 mas, corresponding to the distance of 244±10 pc from the Sun, although the life time of the maser features are only 6 months. The absolute proper motions of the H2O maser features associated with Orion KL and NGC 1333 are derived, possibly indicating the outflow motions from the YSOs as well as the systemic motions of the powering sources.