The action occurred because the airline discovered potential structural issues with the Boeing 737s, said Federal Aviation Administration (FAA) spokeswoman Laura Brown.
The airline notified federal regulators earlier Wednesday, Brown said.
The action is the latest development in a story over safety concerns at an airline with a reputation for efficiency. Southwest has had one fatal accident in its 37-year history.
Brown said the FAA expected to provide more details about the grounding later Wednesday.
A grounding of that magnitude would almost certainly disrupt the airline's schedule, but the airline had not released schedule information Wednesday.
The airline did not return a phone call.
The FAA hit Southwest last Thursday with a $10.2 million fine, the largest in the agency's history, for intentionally flying at least 46 jets without performing required critical safety checks for fuselage cracks.
The agency acknowledged that at least one of its officials bore some responsibility because the unnamed inspector had failed to adequately oversee the carrier.
The airline and the FAA are under investigation by the Department of Transportation's inspector general because of allegations by two whistle-blowers that Southwest was allowed to bypass safety regulations.
The whistle-blowers alleged that Southwest had problems keeping up with critical safety inspections for several years, but they were blocked in attempts to investigate the issue.
Both men alleged that they faced retribution from other FAA employees for trying to enforce basic rules at the airline.
The allegations were uncovered by an investigation by the House Transportation Committee.
Last week, Chairman Jim Oberstar, D-Minn., said his committee had uncovered the most egregious breakdown of airline oversight he had seen in 23 years.
Southwest CEO Gary Kelly announced Tuesday that the airline had suspended three employees after receiving preliminary results of an internal investigation. The investigation had raised "concerns" about the airline's maintenance program, Kelly said.
Southwest operates the largest fleet of 737s in the world. It had 481 of the jets as of December 2006, according to the Air Transport Association.
By Alan Levin, USA TODAY
Text of release from Southwest Airlines Media Relations
SOUTHWEST AIRLINES CONTINUES INTERNAL INVESTIGATION AND AUDIT
Airline Makes the Decision to Temporarily Remove 38 Aircraft
from Scheduled Service
DALLAS - March 12, 2008 - Yesterday, Southwest Airlines CEO Gary Kelly said the airline is taking action on preliminary findings of its own internal investigation into allegations that it violated FAA regulations in March 2007. Kelly vowed to make any changes necessary to ensure that the airline is in full compliance with FAA Airworthiness Directives and all of its own maintenance programs, policies, and procedures.
During last night's review by Southwest of its maintenance records, the airline discovered an ambiguity related to required testing. Southwest made the decision to take a conservative approach and remove aircraft out of scheduled service. Southwest immediately began reinspecting those aircraft. A total of 44 aircraft were affected-one was already retired, five were in maintenance for scheduled checks, and the remaining 38 were removed from scheduled service.
Southwest's decision to remove aircraft from service resulted in approximately four percent of today's Southwest flights being canceled. Due to good weather conditions, the decision caused minimal schedule disruptions and the airline is running more than 90 percent ontime.
A portion of the aircraft have been inspected, cleared, and returned to service. The airline expects to have all of these aircraft inspected by early this evening. The ongoing internal review of Southwest's maintenance programs, policies, and procedures could potentially create other operational changes if the airline needs to swap or reroute aircraft as the internal investigation and audit unfolds.
"Again, we are mindful that during Southwest's 37-year proud history, we have safely transported the population of the United States-every man, woman, and child-four and a half times over. This is a fact. We have been a safe Company. I believe we are a safe Company. I am committed to making sure we become safer still," said Southwest CEO Gary Kelly.