In this research, we propose a methodology to develop OD matrices using mobile phone Call Detail Records (CDR) and limited traffic counts. CDR, which consist of time stamped tower locations with caller IDs, are analyzed first and trips occurring within certain time windows are used to generate tower-to-tower transient OD matrices for different time periods. These are then associated with corresponding nodes of the traffic network and converted to node-to-node transient OD matrices. The actual OD matrices are derived by scaling up these node-to-node transient OD matrices. An optimization based approach, in conjunction with a microscopic traffic simulation platform, is used to determine the scaling factors that result best matches with the observed traffic counts. The methodology is demonstrated using CDR from 2.87 million users of Dhaka, Bangladesh over a month and traffic counts from 13 key locations over 3 days of that month. The applicability of the methodology is supported by a validation study.