Gates toured U.S. bases and met with troops in the thick of the fighting in Kandahar city and the Taliban haven of Zhari district, west of the city.
"I come away from my visits down here today encouraged," Gates told reporters traveling with him. He said that signs of progress were incremental but growing.
Still, he added, "Everybody knows this is far from a done deal."
With the last of the 30,000 U.S. reinforcements arriving in Afghanistan, Gates wanted a firsthand look at operations in the dangerous south where Afghan and international troops are ramping up security.
He traveled to Kandahar province, a region where U.S., Afghan and NATO forces are trying to rout insurgents from their strongholds and bolster the government. The Taliban are fighting back, waging a fear and intimidation campaign to keep local Afghans from siding with international forces and the Afghan government.
"You guys are in the forward foxhole and what makes a difference in the whole campaign is your success here in Kandahar city," Gates told U.S. troops at Camp Nathan Smith, headquarters for U.S. operations in the largest city in southern Afghanistan.
Kandahar is Afghanistan's second-largest city and a linchpin of the retailored battle plan President Barack Obama announced last year. The region is the birthplace of the Taliban and has never been under full control of the U.S.-backed central government in Kabul.
Military commanders know the nearly nine-year war cannot be won without a turnaround in Kandahar, yet goals and plans for the fight there have been vague.
The bulked-up force is meant to blunt Taliban momentum on their home ground and set the stage for a gradual U.S. exit from the war beginning next summer.
Gates spoke with a couple dozen U.S. service members in a courtyard ringed with heavily armored all-terrain vehicles designed to help them survive the homemade bombs that are the biggest death threat to coalition troops. They were part of the 1st Brigade Combat Team, 4th Infantry Division, which arrived Aug. 18, and has already lost eight soldiers - seven last Monday alone.
"Unfortunately, there are going to be more tough days ahead," Gates said. "You know that better than anybody."
One soldier asked Gates why the U.S. doesn't go after insurgents hiding in neighboring Pakistan. The United States is pressing Islamabad to expand its pursuit of insurgents farther into North Waziristan, a border area next to Afghanistan often described as lawless.
"I think the likelihood of direct U.S. military engagement in Pakistan is very low," Gates said.
For the past 18 months, Pakistan has realized the importance of fighting insurgents on its soil and has effectively squeezed militant groups - in some cases, concentrating them in the border area of North Waziristan. U.S. officials are looking for assurances that Pakistan will not end its efforts there because of the demands created by this year's historic floods.
"Everyone understands that the sanctuaries on the other side of the border are a big problem" and the joint U.S.-Pakistan objective is to expunge those hideouts, Gates said. "Unfortunately the flooding in Pakistan is going to delay any operation in North Waziristan for some time."
From Camp Nathan Smith, Gates traveled west of Kandahar to violent Zhari district, which Lt. Gen. David Rodriguez calls "one of the critical districts" outside the city.
Speaking to reporters, Rodriguez predicted that U.S. and Afghan forces will be able to show some progress in Kandahar province before the end of the year and in time for an important end-of-year evaluation of the war by the Obama administration.
Rodriguez would not characterize the expected progress as significant. He said it would be piecemeal and gradual.
For instance, by the end of the year, Rodriguez predicted that Afghans would feel less intimidation from insurgents and local governing councils would be better representative of the people and less dominated by local powerbrokers.
The Obama administration plans a top-to-bottom assessment of the war in December. The review will question whether the strategy Obama laid out is working.