HIAL said Inverness, the group's busiest airport, recorded 3.4% growth by handling 614,302 passengers as it was helped by the popularity of flybe's Amsterdam service.
Of the other sites showing rising figures, Sumburgh was the fastest growing, up 13.2% to 199,583, followed by Barra at 9%, Tiree at 6.8%, Campbeltown at 5.9%, Wick John O'Groats at 5.1% and Islay at 0.2%.
Dundee reported the largest fall in passengers, down 11.2% at 55,531, with Benbecula down 1.6%, Stornoway 1% and Kirkwall down by 0.1%.
Inglis Lyon, managing director of HIAL, said: "We are very pleased with our growth record in 2012, particularly given the difficult economic conditions of the past year.
"There has been a marked growth in oil-related traffic at Sumburgh and Wick John O'Groats, while Inverness has continued to benefit from the success of its Amsterdam service.
"There is clearly more work to do to attract new services to Dundee and we have been in discussion with a number of carriers. However, given the prevailing economic conditions, it is likely to be some time before we make progress."
Figures for December showed a 4.4% increase to 94,707 passengers carried across the group.
Wick John O'Groats reported a 91.1% increase thanks to oil-related helicopter and fixed wing traffic, with the energy sector also a big factor in the 41.3% growth at Sumburgh.
Barra, Kirkwall and Tiree all recorded double-digit percentage growth in December. However, Dundee saw numbers drop 52.8% as Loganair services to Belfast and Birmingham were withdrawn. Inverness was down 4.3% that month, which HIAL said was because of schedule changes and weather-related cancellations.