A multiple mode digitization system for a non-destructive inspection instrument which makes use of a multiplexing circuit and a single set of analog to digital converters to efficiently digitize analog test signals from a plurality of inputs. In the preferred embodiment, each of the analog to digital converters in the system is driven with an independent and separate clock signal, allowing for propagation delay compensation among the plurality of test signals as well as interleaved sampling such that custom sampling rates can be used for each input without the need for more than one clock frequency. In an alternate embodiment, phase adjustments on the sampling clocks are used only for interleave sampling, and digital filters are used to provide signal propagation delay compensation.