We present a novel algorithm, Compact Kd-Trees (CompactKdt), that achieves state-of-the-art performance in searching large scale object image collections. The algorithm uses an order of magnitude less storage and computations by making use of both the full local features (e.g. SIFT) and their compact binary signatures to build and search the K-Tree. We compare classical PCA dimensionality reduction to three methods for generating compact binary representations for the features: Spectral Hashing, Locality Sensitive Hashing, and Locality Sensitive Binary Codes. CompactKdt achieves significant performance gain over using the binary signatures alone, and comparable performance to using the full features alone. Finally, our experiments show significantly better performance than the state-of-the-art Bag of Words (BoW) methods with equivalent or less storage and computational cost.