In a multi-cylinder variable valve lift (VVL) engine, in spite of its high efficiency and low emission performance, operation of the variable valve lift brings about not only variation of the air-fuel ratio at the exhaust manifold, but also individual cylinder air-fuel ratio maldistribution. In this study, in order to reduce the air-fuel ratio variation and maldistribution, we propose an individual cylinder air-fuel ratio estimation algorithm for individual cylinder air-fuel ratio control. For the purpose of the individual cylinder air-fuel ratio estimation, air charging dynamics are modeled according to valve lift conditions. In addition, based on the air charging model, individual cylinder air-fuel ratios are estimated by multi-rate sampling from single universal exhaust gas oxygen (UEGO) sensor located on the exhaust manifold. Estimation results are validated with a one-dimensional engine simulation tool. The results of this study indicate that the estimated air-fuel ratios of the individual cylinders closely followed the experimental individual cylinder air-fuel ratios.