Penicuik House as built by Sir James Clerk was of seven bays and three storeys, piano nobile over attic and basement. Its plan was formal and symmetrical and it was faced with finely dressed ashlar all round. It was covered with an almost flat lead roof, the entrance front carried a fully formed hexastyle portico, unique in Scotland at the time while the garden front had only a plain three bay centerpiece topped by a shallow and extremely austere open pediment.
The masonry, in ashlar, rubble and clamp-fired bricks, and the joinery works were of the highest quality. Much of the masonry remains sound despite a century of unintended exposure to the weather. The structural timbers have gone leaving only a few fragments of the joinery clinging to the shell. Some of the brick vaults survive at ground level. The rooms at principal and attic levels in the south west corner of the plan also had brick vaults, possibly for muniments. The kitchens appear to have been in the north west corner of the basement.
At some point since 1899 action was taken to preserve the wall heads by cement capping. Further remedial and clearance work was carried out in 1988/9.