Traffic state estimation plays an important role in facilitating effective traffic management. This study develops a combinatorial approach for nonparametric short-term queue length estimation in terms of cycle-by-cycle partially observed queues from probe vehicles. The method does not assume random arrivals and does not assume any primary parameters or estimation of any parameters but uses simple algebraic expressions that only depend on signal timing. For an approach lane at a traffic intersection, the conditional queue lengths given probe vehicle location, count, time, and analysis interval (e.g., at the end of red signal phase) are represented by a Negative Hypergeometric distribution. The estimators obtained are compared with parametric methods and simple highway capacity manual methods using field test data involving probe vehicles. The analysis indicates that the nonparametric methods presented in this paper match the accuracy of parametric methods used in the field test data for estimating queue lengths.