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This paper outlines the time jitter effect of a sampling clock on a Software Defined Radio (SDR) technology- based-Digital Intermediate Frequency (IF) transceiver for a mobile communication base station. The implemented Digital IF transceiver is reconfigurable to three bandwidth profiles : 1.75 MHz, 3.5 MHz, and 7 MHz each incorporating the IEEE 802.16d Worldwide Interoperability for Microwave Access (WiMAX) standard and High-Speed Downlink Packet Access (HSDPA) standard. This transceiver can be reconfigured to other standard profiles through software downloaded onto identical hardware platforms, without changing any components or parts on board. This paper examines the relationship between the Signal-to- Noise Ratio (SNR) characteristics of a Digital IF transceiver with an under-sampling scheme and the sampling jitter effect on a multi-channel OFDM signal and a multi-code CDMA signal. The experimental results show that the SNR of the multi-channel OFDM system is more susceptible to sampling clock jitter compared to a multi-code HSDPA system.