The machine's instruction set was increased from the 7 of the SSEM to 26 initially, including multiplication done in hardware. This increased to 30 instructions in the Final Specification version. Ten bits of each word were allocated to hold the instruction code. The standard instruction time was 1.8 milliseconds, but multiplication was much slower, depending on the size of the operand.
The machine's most significant innovation is generally considered to be its incorporation of index registers, commonplace on modern computers. The SSEM had included two registers, implemented as Williams tubes; the accumulator (A) and the program counter (C). As A and C had already been assigned, the tube holding the two index registers, originally known as B-lines, was given the name B. The contents of the registers could be used to modify program instructions, allowing convenient iteration through an array of numbers stored in memory. The Mark 1 also had a fourth tube, (M), to hold the multiplicand and multiplier for a multiplication operation.