Purpose. Dual layer MLC (DMLC) has have been adopted in several commercial products and one major challenge in DMLC usage is leaf sequencing for intensity-modulated radiation therapy (IMRT). In this study we developed a leaf sequencing algorithm for IMRT with an orthogonal DMLC.Methods and Materials. This new algorithm is inspired by the algorithm proposed by Dai and Zhu for IMRT with single layer MLC (SMLC). It iterately determines a delivery segment intensity and corresponding segment shape for a given fluence matrix and leaves residual fluence matrix to following iterations. The segment intensity is determined according to complexities of residual fluence matrix when segment intensity varies from one to highest level in the matrix. The segment intensity and corresponding segment shape that result least complexity was selected. Although the algorithm framework is similar to Dai and Zhu's algorithm, this new algorithm develops complexity algorithms along with rules for determining segment leaf settings when delivered with orthogonal DMLC. This algorithm has been evaluated with 9 groups of randomly generated fluence matrices with various dimensions and intensity levels. Sixteen fluence matrices generated in Pinnacle system for two clinical IMRT examples were also used for evaluation. Statistical information of leaf sequences generated with this algorithm for both the random and clinical matrices were compared to the results of two typical algorithms for SMLC: that proposed by Dai and Zhu and that proposed by Bortfled.Results. Compared to the SMLC delivery sequences generated with Dai and Zhu's algorithm, the proposed algorithm for orthogonal DMLC delivery reduces the average number of segments by 27.7% ∼ 41.8% for 9 groups of randomly generated fluence matrices and 10.5% ∼ 41.7% for clinical ones. When comparing MU efficiency between different algorithms, it is observed that the proposed algorithm performs better than the optimal efficiency of SMLC delivery when dealing with simple fluence matrices, but slightly worse when handling complex ones.Conclusion. This new algorithm generates leaf sequences for orthogonal DMLC delivery with high delivery efficiency in terms of number of leaf segments. This algorithm has potential to work well with orthogonal DMLC for improving efficiency or quality of IMRT.