E-commerce revenue registered another healthy gain for Barnes & Noble Inc. in the third quarter, but higher Nook development costs continue to take a toll on profitability.

For the third quarter of fiscal 2012 ended Jan. 28, Barnes & Noble, No. 41 in the Internet Retailer Top 500 Guide, reported:

• E-commerce sales increased 31.7% to $420 million from $319 million in the third quarter of fiscal 2011.
• Nook sales, which include e-readers, digital content and related accessories, grew year over year about 38% to $542 million from $393 million, the retailer says. Total sales increased 4.7% to $2.43 billion from $2.32 billion.
• Comparable-store sales increased 2.8%.
• Net income was flat at about $52 million.

The web accounted for 17.3% of total sales compared with 13.8% in the third quarter of fiscal 2011. “Our Nook digital content business continues to grow rapidly,” says CEO William Lynch.

For the first nine months:

• E-commerce sales increased 28.7% to $824.4 million from $640.8 in the first three third quarters of fiscal 2011.
• Total sales increased 2.3% to $5.75 billion from $5.62 billion.
• Net loss was $11.1 million compared with a net loss of $14.5 million through the first nine months of fiscal 2011.

The web accounted for 14.3% of total sales compared with 11.4% in the first three quarters of fiscal 2011.

Barnes & Noble will break out its year-end earnings in June and is expecting to end fiscal 2012 with a big jump in e-commerce and Nook sales. For fiscal 2012, total Nook business sales are expected to be about $1.5 billion while total e-commerce sales are expected to grow between 40% and 50%, although the retailer didn’t release an actual number. Total sales are expected to range from $7 billion to $7.2 billion.